ZNF417

Summary

ZNF417 (zinc finger protein 417, HGNC:20646) is a protein-coding gene on chromosome 19q13.43, encoding Zinc finger protein 417 (Q8TAU3). May be involved in transcriptional regulation.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus.

Source: NCBI Gene 147687 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 107 total
• MANE Select transcript: NM_152475

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20646
Approved symbol	ZNF417
Name	zinc finger protein 417
Location	19q13.43
Locus type	gene with protein product
Status	Approved
Aliases	MGC34079
Ensembl gene	ENSG00000173480
Ensembl biotype	protein_coding
OMIM	621276
Entrez	147687

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000312026, ENST00000594396, ENST00000595559, ENST00000597515, ENST00000598526, ENST00000598629, ENST00000599251

RefSeq mRNA: 2 — MANE Select: NM_152475 NM_001297734, NM_152475

CCDS: CCDS12965, CCDS74469

Canonical transcript exons

ENST00000312026 — 3 exons

Exon	Start	End
ENSE00001431532	57905774	57910114
ENSE00003214830	57916379	57916592
ENSE00003654141	57912060	57912189

Expression profiles

Bgee: expression breadth ubiquitous, 174 present calls, max score 90.81.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.7058 / max 55.9687, expressed in 1688 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
182919	6.7058	1688

Top tissues by expression

232 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	90.81	gold quality
cerebellar hemisphere	UBERON:0002245	89.82	gold quality
cerebellar cortex	UBERON:0002129	89.53	gold quality
cortical plate	UBERON:0005343	89.44	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.18	gold quality
right uterine tube	UBERON:0001302	87.71	gold quality
right lobe of thyroid gland	UBERON:0001119	87.30	gold quality
pituitary gland	UBERON:0000007	87.22	gold quality
left lobe of thyroid gland	UBERON:0001120	86.97	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.75	gold quality
cerebellum	UBERON:0002037	86.09	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.03	gold quality
anterior cingulate cortex	UBERON:0009835	86.02	gold quality
ganglionic eminence	UBERON:0004023	85.98	gold quality
right frontal lobe	UBERON:0002810	85.37	gold quality
thyroid gland	UBERON:0002046	85.33	gold quality
apex of heart	UBERON:0002098	85.30	gold quality
lower esophagus mucosa	UBERON:0035834	85.11	gold quality
spleen	UBERON:0002106	85.07	gold quality
minor salivary gland	UBERON:0001830	84.94	gold quality
right lobe of liver	UBERON:0001114	84.76	gold quality
mucosa of transverse colon	UBERON:0004991	84.64	gold quality
gall bladder	UBERON:0002110	84.62	gold quality
calcaneal tendon	UBERON:0003701	84.19	gold quality
hypothalamus	UBERON:0001898	83.98	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.96	gold quality
lower esophagus muscularis layer	UBERON:0035833	83.69	gold quality
lower esophagus	UBERON:0013473	83.68	gold quality
small intestine Peyer’s patch	UBERON:0003454	83.61	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	83.56	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.29

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
CDKN2A

JASPAR motifs

Motif	Name	Family
MA1727.1	ZNF417	Factors with multiple dispersed zinc fingers
MA1727.2	ZNF417	Factors with multiple dispersed zinc fingers

JASPAR matrix evidence (PMIDs): PMID:32923624

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

97 targeting ZNF417, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-1273H-5P	99.77	66.32	2471
HSA-MIR-548AG	99.77	69.25	1492
HSA-MIR-149-3P	99.72	68.22	3963

Cross-species orthologs

0 orthologs

Paralogs (51): WIZ (ENSG00000011451), ZNF416 (ENSG00000083817), MYNN (ENSG00000085274), PRDM4 (ENSG00000110851), PRDM2 (ENSG00000116731), ZBTB17 (ENSG00000116809), ZNF644 (ENSG00000122482), GZF1 (ENSG00000125812), ZNF426 (ENSG00000130818), ZNF287 (ENSG00000141040), ZNF697 (ENSG00000143067), ZNF687 (ENSG00000143373), ZNF214 (ENSG00000149050), ZNF547 (ENSG00000152433), ZNF776 (ENSG00000152443), ZNF230 (ENSG00000159882), ZNF222 (ENSG00000159885), ZNF233 (ENSG00000159915), ZNF333 (ENSG00000160961), ZNF319 (ENSG00000166188), ZNF592 (ENSG00000166716), ZNF646 (ENSG00000167395), ZNF507 (ENSG00000168813), ZNF768 (ENSG00000169957), ZNF408 (ENSG00000175213), ZBTB41 (ENSG00000177888), ZNF223 (ENSG00000178386), ZNF852 (ENSG00000178917), ZNF784 (ENSG00000179922), ZNF572 (ENSG00000180938), ZNF707 (ENSG00000181135), ZNF746 (ENSG00000181220), ZNF467 (ENSG00000181444), ZNF530 (ENSG00000183647), ZNF17 (ENSG00000186272), ZNF527 (ENSG00000189164), ZKSCAN7 (ENSG00000196345), ZNF34 (ENSG00000196378), ZNF774 (ENSG00000196391), ZNF777 (ENSG00000196453)

Protein

Protein identifiers

Zinc finger protein 417 — Q8TAU3 (reviewed: Q8TAU3)

All UniProt accessions (7): Q8TAU3, M0QXH9, M0R0M6, M0R0V5, M0R178, M0R230, M0R267

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in transcriptional regulation.

Subcellular location. Nucleus.

Similarity. Belongs to the krueppel C2H2-type zinc-finger protein family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8TAU3-1	1	yes
Q8TAU3-2	2

RefSeq proteins (2): NP_001284663, NP_689688* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR013087	Znf_C2H2_type	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR036236	Znf_C2H2_sf	Homologous_superfamily
IPR050758	Znf_C2H2-type	Family

Pfam: PF00096, PF01352

UniProt features (21 total): zinc finger region 13, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TAU3-F1	64.65	0.21

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-212436	Generic Transcription Pathway

MSigDB gene sets: 37 (showing top): GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, DIDO1_TARGET_GENES, PRKDC_TARGET_GENES, SETD7_TARGET_GENES, TAFAZZIN_TARGET_GENES, ZNF197_TARGET_GENES, ZNF350_TARGET_GENES, ZNF362_TARGET_GENES, ZNF597_TARGET_GENES, MIR340_5P, LET_7C_3P

GO Biological Process (3): regulation of transcription by RNA polymerase II (GO:0006357), negative regulation of DNA-templated transcription (GO:0045892), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), zinc ion binding (GO:0008270), DNA binding (GO:0003677), protein binding (GO:0005515), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837)

GO Cellular Component (1): nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
RNA Polymerase II Transcription	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
negative regulation of RNA biosynthetic process	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transition metal ion binding	1
nucleic acid binding	1
binding	1
cation binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

584 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZNF417	OR8D2	Q9GZM6	624
ZNF417	GRIP2	Q9C0E4	479
ZNF417	GLRA2	P23416	448
ZNF417	OR51M1	Q9H341	447
ZNF417	CCDC74A	Q96AQ1	444
ZNF417	OR1C1	Q15619	390
ZNF417	PHOSPHO2	Q8TCD6	375
ZNF417	G3V325	G3V325	371
ZNF417	CLHC1	Q8NHS4	370
ZNF417	LRRC66	Q68CR7	369
ZNF417	OR2T35	Q8NGX2	359
ZNF417	KIAA1328	Q86T90	350
ZNF417	FABP6	P51161	348
ZNF417	AADAT	Q8N5Z0	348
ZNF417	VN1R1	Q9GZP7	348

IntAct

637 interactions, top by confidence:

A	B	Type	Score
ZNF417	TRIM27	psi-mi:“MI:0915”(physical association)	0.780
ZNF417	MDFI	psi-mi:“MI:0915”(physical association)	0.780
MDFI	ZNF417	psi-mi:“MI:0915”(physical association)	0.780
TNS2	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
FSD2	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
STX11	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
KRT38	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
KRTAP5-9	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-7	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
KRTAP10-8	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
GOLGA2	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	KRT40	psi-mi:“MI:0915”(physical association)	0.720
HMBOX1	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	ADAMTSL4	psi-mi:“MI:0915”(physical association)	0.720
CEP70	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
TRIM41	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
ZBTB8A	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
KXD1	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
LZTS2	ZNF417	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	TRIM54	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	MID2	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	FSD2	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	KRTAP5-9	psi-mi:“MI:0915”(physical association)	0.720
ZNF417	KRTAP10-7	psi-mi:“MI:0915”(physical association)	0.720

BioGRID (220): ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid), ZNF417 (Two-hybrid)

ESM2 similar proteins: A0JNB1, A1YF12, A1YG88, A2T759, A3KN32, B2RUI1, O43296, O75123, P10072, P17020, P17097, P51814, P52736, P52740, Q07230, Q08ER8, Q13398, Q14590, Q32KN0, Q3KQV3, Q3MIS6, Q4V8A8, Q5CZA5, Q5RBQ3, Q5RBX0, Q5RCD9, Q5RCX4, Q6GQR8, Q6NX45, Q6P9A3, Q6PK81, Q7TSH9, Q7TSI0, Q7Z7L9, Q86UD4, Q8BFS8, Q8BLB0, Q8IVP9, Q8IZ26, Q8N9F8

Diamond homologs: A2RRD8, A6NFI3, A6NM28, A8MUZ8, A8MWA4, B2RUI1, B4DU55, E9Q8G5, O43296, O43361, O75467, O75820, P0CH99, P0CI00, P10078, P16373, P16374, P17021, P17023, P17032, P17097, P17098, P21506, P51786, P52740, Q06732, Q08ER8, Q13106, Q13360, Q13398, Q14592, Q147U1, Q32M78, Q3KQV3, Q3MIS6, Q3SY52, Q571J5, Q5CZA5, Q5HY98, Q5R7I8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 66 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Keratinization	9	14.3×	1e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

107 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	89
Likely benign	10
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1052 predictions. Top by Δscore:

Variant	Effect	Δscore
19:57916377:A:AT	donor_loss	1.0000
19:57916377:AC:A	donor_loss	1.0000
19:57916378:C:CT	donor_loss	1.0000
19:57916378:CC:C	donor_loss	1.0000
19:57915568:A:AC	donor_gain	0.9700
19:57915569:C:CC	donor_gain	0.9700
19:57916377:A:AC	donor_gain	0.9500
19:57916378:C:CC	donor_gain	0.9500
19:57910112:AACCT:A	acceptor_loss	0.9400
19:57910113:ACCTG:A	acceptor_loss	0.9400
19:57910115:C:CA	acceptor_loss	0.9400
19:57910116:T:A	acceptor_loss	0.9400
19:57914990:C:A	acceptor_gain	0.9400
19:57910111:CAAC:C	acceptor_gain	0.9300
19:57915569:CTGA:C	donor_gain	0.9300
19:57912052:CAACT:C	donor_loss	0.9100
19:57912053:AACTT:A	donor_loss	0.9100
19:57912054:ACTTA:A	donor_loss	0.9100
19:57912055:CTTAC:C	donor_loss	0.9100
19:57912056:TT:T	donor_loss	0.9100
19:57912056:TTA:T	donor_loss	0.9100
19:57912057:TA:T	donor_loss	0.9100
19:57912059:C:CA	donor_loss	0.9100
19:57912059:C:T	donor_loss	0.9100
19:57912185:CCCTG:C	acceptor_gain	0.9100
19:57912186:CCTGC:C	acceptor_gain	0.9100
19:57912187:CTG:C	acceptor_gain	0.9100
19:57912051:GCAAC:G	donor_loss	0.9000
19:57915955:C:T	acceptor_gain	0.9000
19:57911431:C:CA	donor_gain	0.8900

AlphaMissense

3826 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:57909111:A:C	F389L	0.997
19:57909111:A:T	F389L	0.997
19:57909113:A:G	F389L	0.997
19:57909027:A:C	F417L	0.995
19:57909027:A:T	F417L	0.995
19:57909029:A:G	F417L	0.995
19:57909084:A:C	H398Q	0.995
19:57909084:A:T	H398Q	0.995
19:57908691:A:C	F529L	0.994
19:57908691:A:T	F529L	0.994
19:57908693:A:G	F529L	0.994
19:57908775:A:C	F501L	0.993
19:57908775:A:T	F501L	0.993
19:57908777:A:G	F501L	0.993
19:57908607:A:C	F557L	0.992
19:57908607:A:T	F557L	0.992
19:57908609:A:G	F557L	0.992
19:57908943:A:C	F445L	0.991
19:57908943:A:T	F445L	0.991
19:57908945:A:G	F445L	0.991
19:57909086:G:C	H398D	0.991
19:57909072:A:C	H402Q	0.990
19:57909072:A:T	H402Q	0.990
19:57909082:T:G	Q399P	0.988
19:57909086:G:T	H398N	0.988
19:57909094:A:G	L395P	0.987
19:57909363:A:C	F305L	0.987
19:57909363:A:T	F305L	0.987
19:57909365:A:G	F305L	0.987
19:57909000:G:C	H426Q	0.986

dbSNP variants (sampled 300 via entrez): RS1000070826 (19:57917743 G>C), RS1000513626 (19:57917953 T>C), RS1000751349 (19:57908465 C>G), RS1001311378 (19:57917453 C>T), RS1001800470 (19:57913610 G>C), RS1001924668 (19:57908261 G>A), RS1002059149 (19:57914566 CAT>C), RS1002313672 (19:57908910 T>A,G), RS1002538655 (19:57907150 C>A), RS1002692368 (19:57912476 G>A,T), RS1004051834 (19:57911487 G>T), RS1004326513 (19:57911806 C>T), RS1004346521 (19:57906442 G>A), RS1004505010 (19:57914094 TGTCAGCTGATGCAGC>T), RS1005521042 (19:57918207 A>G)

Disease associations

OMIM: gene MIM:621276 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST006427_4	Depression in smokers	1.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
TAK-243	increases sumoylation	1
benzo(e)pyrene	decreases methylation	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
Arsenic	affects methylation	1
Atrazine	increases expression	1
Cadmium	increases abundance, increases expression	1
Methapyrilene	decreases methylation	1
Urethane	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	increases abundance, increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.